Multiple sequence alignment - TraesCS2B01G343000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G343000 chr2B 100.000 3509 0 0 1 3509 489005003 489001495 0.000000e+00 6481
1 TraesCS2B01G343000 chr2B 96.939 98 1 2 3322 3419 525815563 525815658 2.800000e-36 163
2 TraesCS2B01G343000 chr2B 87.302 126 12 4 3301 3424 402218147 402218024 1.310000e-29 141
3 TraesCS2B01G343000 chr2A 91.497 3152 196 34 204 3325 572810787 572813896 0.000000e+00 4270
4 TraesCS2B01G343000 chr2A 93.000 100 1 1 3416 3509 572813899 572813998 1.310000e-29 141
5 TraesCS2B01G343000 chr2D 95.498 2399 89 7 945 3325 417092426 417090029 0.000000e+00 3814
6 TraesCS2B01G343000 chr2D 98.936 94 1 0 3416 3509 417090026 417089933 6.020000e-38 169
7 TraesCS2B01G343000 chr2D 97.895 95 1 1 3326 3420 503441313 503441220 2.800000e-36 163
8 TraesCS2B01G343000 chr6A 97.872 94 0 2 3332 3424 563554408 563554316 1.010000e-35 161
9 TraesCS2B01G343000 chr5B 98.889 90 1 0 3332 3421 45261635 45261724 1.010000e-35 161
10 TraesCS2B01G343000 chr5B 92.793 111 3 5 3317 3424 482285845 482285953 4.690000e-34 156
11 TraesCS2B01G343000 chr4D 100.000 86 0 0 3332 3417 481440702 481440617 3.630000e-35 159
12 TraesCS2B01G343000 chr1D 92.793 111 4 4 3331 3441 474055590 474055696 1.300000e-34 158
13 TraesCS2B01G343000 chr3B 94.949 99 5 0 3325 3423 98989461 98989363 4.690000e-34 156


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G343000 chr2B 489001495 489005003 3508 True 6481.0 6481 100.0000 1 3509 1 chr2B.!!$R2 3508
1 TraesCS2B01G343000 chr2A 572810787 572813998 3211 False 2205.5 4270 92.2485 204 3509 2 chr2A.!!$F1 3305
2 TraesCS2B01G343000 chr2D 417089933 417092426 2493 True 1991.5 3814 97.2170 945 3509 2 chr2D.!!$R2 2564

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
143 144 0.108329 CACGGGGCTCACGTTTCTAT 60.108 55.0 0.0 0.0 43.58 1.98 F
575 579 0.321671 AGTACGCACATGGCTCAAGT 59.678 50.0 0.0 0.0 41.67 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 1995 0.839946 ATCCCTTCATGAACCCTCCG 59.160 55.0 3.38 0.0 0.00 4.63 R
2516 2521 1.588239 ATGAGGCTCCATTGAGGTCA 58.412 50.0 12.86 0.0 39.14 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.445193 CTCGTCTTTATACTTTCGTACTTGTT 57.555 34.615 0.00 0.00 0.00 2.83
26 27 8.801715 TCGTCTTTATACTTTCGTACTTGTTT 57.198 30.769 0.00 0.00 0.00 2.83
27 28 8.905702 TCGTCTTTATACTTTCGTACTTGTTTC 58.094 33.333 0.00 0.00 0.00 2.78
28 29 8.693504 CGTCTTTATACTTTCGTACTTGTTTCA 58.306 33.333 0.00 0.00 0.00 2.69
36 37 8.751302 ACTTTCGTACTTGTTTCATTGTTTTT 57.249 26.923 0.00 0.00 0.00 1.94
37 38 8.856247 ACTTTCGTACTTGTTTCATTGTTTTTC 58.144 29.630 0.00 0.00 0.00 2.29
38 39 7.425915 TTCGTACTTGTTTCATTGTTTTTCG 57.574 32.000 0.00 0.00 0.00 3.46
39 40 5.966503 TCGTACTTGTTTCATTGTTTTTCGG 59.033 36.000 0.00 0.00 0.00 4.30
40 41 5.740099 CGTACTTGTTTCATTGTTTTTCGGT 59.260 36.000 0.00 0.00 0.00 4.69
41 42 6.251801 CGTACTTGTTTCATTGTTTTTCGGTT 59.748 34.615 0.00 0.00 0.00 4.44
42 43 7.201367 CGTACTTGTTTCATTGTTTTTCGGTTT 60.201 33.333 0.00 0.00 0.00 3.27
43 44 6.826612 ACTTGTTTCATTGTTTTTCGGTTTG 58.173 32.000 0.00 0.00 0.00 2.93
44 45 5.786401 TGTTTCATTGTTTTTCGGTTTGG 57.214 34.783 0.00 0.00 0.00 3.28
45 46 4.093556 TGTTTCATTGTTTTTCGGTTTGGC 59.906 37.500 0.00 0.00 0.00 4.52
46 47 3.810310 TCATTGTTTTTCGGTTTGGCT 57.190 38.095 0.00 0.00 0.00 4.75
47 48 4.130286 TCATTGTTTTTCGGTTTGGCTT 57.870 36.364 0.00 0.00 0.00 4.35
48 49 3.868077 TCATTGTTTTTCGGTTTGGCTTG 59.132 39.130 0.00 0.00 0.00 4.01
49 50 3.320673 TTGTTTTTCGGTTTGGCTTGT 57.679 38.095 0.00 0.00 0.00 3.16
50 51 4.451629 TTGTTTTTCGGTTTGGCTTGTA 57.548 36.364 0.00 0.00 0.00 2.41
51 52 4.451629 TGTTTTTCGGTTTGGCTTGTAA 57.548 36.364 0.00 0.00 0.00 2.41
52 53 4.817517 TGTTTTTCGGTTTGGCTTGTAAA 58.182 34.783 0.00 0.00 0.00 2.01
53 54 5.235516 TGTTTTTCGGTTTGGCTTGTAAAA 58.764 33.333 0.00 0.00 0.00 1.52
54 55 5.348997 TGTTTTTCGGTTTGGCTTGTAAAAG 59.651 36.000 0.00 0.00 0.00 2.27
55 56 4.722361 TTTCGGTTTGGCTTGTAAAAGT 57.278 36.364 0.00 0.00 0.00 2.66
56 57 5.831702 TTTCGGTTTGGCTTGTAAAAGTA 57.168 34.783 0.00 0.00 0.00 2.24
57 58 6.394025 TTTCGGTTTGGCTTGTAAAAGTAT 57.606 33.333 0.00 0.00 0.00 2.12
58 59 5.365403 TCGGTTTGGCTTGTAAAAGTATG 57.635 39.130 0.00 0.00 0.00 2.39
59 60 4.822896 TCGGTTTGGCTTGTAAAAGTATGT 59.177 37.500 0.00 0.00 0.00 2.29
60 61 5.299782 TCGGTTTGGCTTGTAAAAGTATGTT 59.700 36.000 0.00 0.00 0.00 2.71
61 62 5.627780 CGGTTTGGCTTGTAAAAGTATGTTC 59.372 40.000 0.00 0.00 0.00 3.18
62 63 5.924254 GGTTTGGCTTGTAAAAGTATGTTCC 59.076 40.000 0.00 0.00 0.00 3.62
63 64 5.365403 TTGGCTTGTAAAAGTATGTTCCG 57.635 39.130 0.00 0.00 0.00 4.30
64 65 4.391155 TGGCTTGTAAAAGTATGTTCCGT 58.609 39.130 0.00 0.00 0.00 4.69
65 66 4.822896 TGGCTTGTAAAAGTATGTTCCGTT 59.177 37.500 0.00 0.00 0.00 4.44
66 67 5.151389 GGCTTGTAAAAGTATGTTCCGTTG 58.849 41.667 0.00 0.00 0.00 4.10
67 68 5.278120 GGCTTGTAAAAGTATGTTCCGTTGT 60.278 40.000 0.00 0.00 0.00 3.32
68 69 6.203647 GCTTGTAAAAGTATGTTCCGTTGTT 58.796 36.000 0.00 0.00 0.00 2.83
69 70 7.354257 GCTTGTAAAAGTATGTTCCGTTGTTA 58.646 34.615 0.00 0.00 0.00 2.41
70 71 8.019094 GCTTGTAAAAGTATGTTCCGTTGTTAT 58.981 33.333 0.00 0.00 0.00 1.89
71 72 9.887406 CTTGTAAAAGTATGTTCCGTTGTTATT 57.113 29.630 0.00 0.00 0.00 1.40
76 77 9.974980 AAAAGTATGTTCCGTTGTTATTTTCAT 57.025 25.926 0.00 0.00 0.00 2.57
77 78 9.974980 AAAGTATGTTCCGTTGTTATTTTCATT 57.025 25.926 0.00 0.00 0.00 2.57
78 79 9.620660 AAGTATGTTCCGTTGTTATTTTCATTC 57.379 29.630 0.00 0.00 0.00 2.67
79 80 9.010029 AGTATGTTCCGTTGTTATTTTCATTCT 57.990 29.630 0.00 0.00 0.00 2.40
80 81 9.620660 GTATGTTCCGTTGTTATTTTCATTCTT 57.379 29.630 0.00 0.00 0.00 2.52
82 83 9.840427 ATGTTCCGTTGTTATTTTCATTCTTAG 57.160 29.630 0.00 0.00 0.00 2.18
83 84 8.293867 TGTTCCGTTGTTATTTTCATTCTTAGG 58.706 33.333 0.00 0.00 0.00 2.69
84 85 6.848451 TCCGTTGTTATTTTCATTCTTAGGC 58.152 36.000 0.00 0.00 0.00 3.93
85 86 6.657541 TCCGTTGTTATTTTCATTCTTAGGCT 59.342 34.615 0.00 0.00 0.00 4.58
86 87 7.175990 TCCGTTGTTATTTTCATTCTTAGGCTT 59.824 33.333 0.00 0.00 0.00 4.35
87 88 7.812669 CCGTTGTTATTTTCATTCTTAGGCTTT 59.187 33.333 0.00 0.00 0.00 3.51
88 89 9.834628 CGTTGTTATTTTCATTCTTAGGCTTTA 57.165 29.630 0.00 0.00 0.00 1.85
109 110 7.867909 GCTTTATTAGTTCAAAGCCAGACTTTT 59.132 33.333 7.63 0.00 46.73 2.27
110 111 9.399403 CTTTATTAGTTCAAAGCCAGACTTTTC 57.601 33.333 0.00 0.00 46.73 2.29
111 112 8.691661 TTATTAGTTCAAAGCCAGACTTTTCT 57.308 30.769 0.00 0.00 46.73 2.52
112 113 7.588497 ATTAGTTCAAAGCCAGACTTTTCTT 57.412 32.000 0.00 0.00 46.73 2.52
113 114 5.921962 AGTTCAAAGCCAGACTTTTCTTT 57.078 34.783 0.00 0.00 46.73 2.52
114 115 5.654497 AGTTCAAAGCCAGACTTTTCTTTG 58.346 37.500 11.68 11.68 46.73 2.77
115 116 4.654091 TCAAAGCCAGACTTTTCTTTGG 57.346 40.909 15.33 0.00 46.73 3.28
121 122 3.982475 CCAGACTTTTCTTTGGCCTTTC 58.018 45.455 3.32 0.00 0.00 2.62
122 123 3.638627 CCAGACTTTTCTTTGGCCTTTCT 59.361 43.478 3.32 0.00 0.00 2.52
123 124 4.261783 CCAGACTTTTCTTTGGCCTTTCTC 60.262 45.833 3.32 0.00 0.00 2.87
124 125 3.891977 AGACTTTTCTTTGGCCTTTCTCC 59.108 43.478 3.32 0.00 0.00 3.71
125 126 3.636764 GACTTTTCTTTGGCCTTTCTCCA 59.363 43.478 3.32 0.00 0.00 3.86
126 127 3.384789 ACTTTTCTTTGGCCTTTCTCCAC 59.615 43.478 3.32 0.00 32.45 4.02
127 128 1.604604 TTCTTTGGCCTTTCTCCACG 58.395 50.000 3.32 0.00 32.45 4.94
128 129 0.250727 TCTTTGGCCTTTCTCCACGG 60.251 55.000 3.32 0.00 32.45 4.94
129 130 1.228429 TTTGGCCTTTCTCCACGGG 60.228 57.895 3.32 0.00 32.45 5.28
130 131 2.706952 TTTGGCCTTTCTCCACGGGG 62.707 60.000 3.32 0.00 32.45 5.73
132 133 4.035102 GCCTTTCTCCACGGGGCT 62.035 66.667 0.00 0.00 39.68 5.19
133 134 2.269241 CCTTTCTCCACGGGGCTC 59.731 66.667 0.00 0.00 0.00 4.70
134 135 2.592993 CCTTTCTCCACGGGGCTCA 61.593 63.158 0.00 0.00 0.00 4.26
135 136 1.376037 CTTTCTCCACGGGGCTCAC 60.376 63.158 0.00 0.00 0.00 3.51
136 137 3.234630 TTTCTCCACGGGGCTCACG 62.235 63.158 0.00 0.00 37.36 4.35
137 138 4.988716 TCTCCACGGGGCTCACGT 62.989 66.667 0.00 0.00 46.82 4.49
138 139 4.003788 CTCCACGGGGCTCACGTT 62.004 66.667 0.00 0.00 43.58 3.99
139 140 3.530910 CTCCACGGGGCTCACGTTT 62.531 63.158 0.00 0.00 43.58 3.60
140 141 3.047877 CCACGGGGCTCACGTTTC 61.048 66.667 0.00 0.00 43.58 2.78
141 142 2.030562 CACGGGGCTCACGTTTCT 59.969 61.111 0.00 0.00 43.58 2.52
142 143 1.290955 CACGGGGCTCACGTTTCTA 59.709 57.895 0.00 0.00 43.58 2.10
143 144 0.108329 CACGGGGCTCACGTTTCTAT 60.108 55.000 0.00 0.00 43.58 1.98
144 145 1.135527 CACGGGGCTCACGTTTCTATA 59.864 52.381 0.00 0.00 43.58 1.31
145 146 1.407979 ACGGGGCTCACGTTTCTATAG 59.592 52.381 0.00 0.00 42.70 1.31
146 147 1.407979 CGGGGCTCACGTTTCTATAGT 59.592 52.381 0.00 0.00 0.00 2.12
147 148 2.620115 CGGGGCTCACGTTTCTATAGTA 59.380 50.000 0.00 0.00 0.00 1.82
148 149 3.549625 CGGGGCTCACGTTTCTATAGTAC 60.550 52.174 0.00 0.00 0.00 2.73
149 150 3.635836 GGGGCTCACGTTTCTATAGTACT 59.364 47.826 0.00 0.00 0.00 2.73
150 151 4.499357 GGGGCTCACGTTTCTATAGTACTG 60.499 50.000 5.39 0.00 0.00 2.74
151 152 4.043073 GGCTCACGTTTCTATAGTACTGC 58.957 47.826 5.39 0.00 0.00 4.40
152 153 4.439700 GGCTCACGTTTCTATAGTACTGCA 60.440 45.833 5.39 0.00 0.00 4.41
153 154 5.100259 GCTCACGTTTCTATAGTACTGCAA 58.900 41.667 5.39 0.00 0.00 4.08
154 155 5.749109 GCTCACGTTTCTATAGTACTGCAAT 59.251 40.000 5.39 0.00 0.00 3.56
155 156 6.916387 GCTCACGTTTCTATAGTACTGCAATA 59.084 38.462 5.39 0.00 0.00 1.90
156 157 7.595502 GCTCACGTTTCTATAGTACTGCAATAT 59.404 37.037 5.39 0.00 0.00 1.28
157 158 9.464714 CTCACGTTTCTATAGTACTGCAATATT 57.535 33.333 5.39 0.00 0.00 1.28
172 173 8.841444 ACTGCAATATTAATTTGTTAGAAGCG 57.159 30.769 0.00 0.00 0.00 4.68
173 174 7.432252 ACTGCAATATTAATTTGTTAGAAGCGC 59.568 33.333 0.00 0.00 0.00 5.92
174 175 7.254137 TGCAATATTAATTTGTTAGAAGCGCA 58.746 30.769 11.47 0.00 0.00 6.09
175 176 7.757173 TGCAATATTAATTTGTTAGAAGCGCAA 59.243 29.630 11.47 0.00 0.00 4.85
176 177 8.755018 GCAATATTAATTTGTTAGAAGCGCAAT 58.245 29.630 11.47 0.00 0.00 3.56
180 181 7.739022 TTAATTTGTTAGAAGCGCAATCATG 57.261 32.000 11.47 0.00 0.00 3.07
200 201 7.034685 TCATGCCACTTATCATGAAAAGATG 57.965 36.000 0.00 0.00 44.08 2.90
201 202 6.829811 TCATGCCACTTATCATGAAAAGATGA 59.170 34.615 0.00 0.00 44.08 2.92
202 203 6.441093 TGCCACTTATCATGAAAAGATGAC 57.559 37.500 0.00 0.00 35.17 3.06
224 225 6.377429 TGACTTCTTGATATAGGAACAGTCGT 59.623 38.462 0.00 0.00 28.32 4.34
229 230 3.246936 TGATATAGGAACAGTCGTCGTCG 59.753 47.826 0.00 0.00 38.55 5.12
234 235 0.975544 GAACAGTCGTCGTCGTCATG 59.024 55.000 1.33 2.67 38.33 3.07
236 237 1.514228 CAGTCGTCGTCGTCATGGG 60.514 63.158 1.33 0.00 38.33 4.00
252 253 3.655777 TCATGGGTACTTTTGGTCTCCTT 59.344 43.478 0.00 0.00 0.00 3.36
263 264 0.978146 GGTCTCCTTGCCTCCTGCTA 60.978 60.000 0.00 0.00 42.00 3.49
274 275 0.531532 CTCCTGCTACCATCTTGGCG 60.532 60.000 0.00 0.00 42.67 5.69
275 276 2.182842 CCTGCTACCATCTTGGCGC 61.183 63.158 0.00 0.00 42.67 6.53
310 312 3.128764 GGCCTCCGATCTTTAAGGTTTTG 59.871 47.826 0.00 0.00 0.00 2.44
331 334 5.830799 TGTGGCATCTATTGGTGATCTAT 57.169 39.130 0.00 0.00 0.00 1.98
379 383 2.890808 TATTTTGCGGTGCCACAAAA 57.109 40.000 16.37 16.37 46.44 2.44
410 414 6.176183 AGGTTTGTGTCCTCAATGATCTTAG 58.824 40.000 0.00 0.00 0.00 2.18
496 500 8.287439 TGTGAAGTTAAAATCTTTCCTTGACA 57.713 30.769 0.00 0.00 0.00 3.58
526 530 8.573885 TGTAAAGATATTATGATTCGACGACCT 58.426 33.333 0.00 0.00 0.00 3.85
528 532 5.955488 AGATATTATGATTCGACGACCTGG 58.045 41.667 0.00 0.00 0.00 4.45
530 534 3.431922 TTATGATTCGACGACCTGGAC 57.568 47.619 0.00 0.00 0.00 4.02
553 557 5.480073 ACTTCTAGGATATCATCACTGGCTC 59.520 44.000 4.83 0.00 0.00 4.70
557 561 4.970711 AGGATATCATCACTGGCTCAAAG 58.029 43.478 4.83 0.00 0.00 2.77
558 562 4.411540 AGGATATCATCACTGGCTCAAAGT 59.588 41.667 4.83 0.00 0.00 2.66
559 563 5.604231 AGGATATCATCACTGGCTCAAAGTA 59.396 40.000 4.83 0.00 0.00 2.24
560 564 5.698545 GGATATCATCACTGGCTCAAAGTAC 59.301 44.000 4.83 0.00 0.00 2.73
574 578 1.442769 AAGTACGCACATGGCTCAAG 58.557 50.000 0.00 0.00 41.67 3.02
575 579 0.321671 AGTACGCACATGGCTCAAGT 59.678 50.000 0.00 0.00 41.67 3.16
586 591 2.867624 TGGCTCAAGTCTTGCATCTTT 58.132 42.857 7.78 0.00 0.00 2.52
593 598 6.349611 GCTCAAGTCTTGCATCTTTTTGGATA 60.350 38.462 7.78 0.00 0.00 2.59
596 601 5.574188 AGTCTTGCATCTTTTTGGATAGGT 58.426 37.500 0.00 0.00 0.00 3.08
688 693 6.978080 TGTTGCTCCAGTCTAATTTTTGTTTC 59.022 34.615 0.00 0.00 0.00 2.78
735 740 7.762588 TTCGTCCTCCAAAAATTAATACCAA 57.237 32.000 0.00 0.00 0.00 3.67
738 743 7.666388 TCGTCCTCCAAAAATTAATACCAAAGA 59.334 33.333 0.00 0.00 0.00 2.52
777 782 7.295952 CAGATACCACTGTGATTCTTAACAC 57.704 40.000 9.86 0.00 37.51 3.32
790 795 7.800380 GTGATTCTTAACACATGACTCACTTTG 59.200 37.037 0.00 0.00 37.70 2.77
791 796 5.673337 TCTTAACACATGACTCACTTTGC 57.327 39.130 0.00 0.00 0.00 3.68
800 805 7.927629 ACACATGACTCACTTTGCATTATTTTT 59.072 29.630 0.00 0.00 0.00 1.94
801 806 8.430063 CACATGACTCACTTTGCATTATTTTTC 58.570 33.333 0.00 0.00 0.00 2.29
803 808 9.844790 CATGACTCACTTTGCATTATTTTTCTA 57.155 29.630 0.00 0.00 0.00 2.10
827 832 9.774742 CTAATCTTAAAATCCAAAGCAGTGTAC 57.225 33.333 0.00 0.00 0.00 2.90
837 842 7.337480 TCCAAAGCAGTGTACGTATAATAGA 57.663 36.000 0.00 0.00 0.00 1.98
838 843 7.423199 TCCAAAGCAGTGTACGTATAATAGAG 58.577 38.462 0.00 0.00 0.00 2.43
840 845 7.919091 CCAAAGCAGTGTACGTATAATAGAGAA 59.081 37.037 0.00 0.00 0.00 2.87
843 848 8.624367 AGCAGTGTACGTATAATAGAGAAGAT 57.376 34.615 0.00 0.00 0.00 2.40
845 850 9.119329 GCAGTGTACGTATAATAGAGAAGATTG 57.881 37.037 0.00 0.00 0.00 2.67
849 854 9.459640 TGTACGTATAATAGAGAAGATTGTTGC 57.540 33.333 0.00 0.00 0.00 4.17
852 857 7.868415 ACGTATAATAGAGAAGATTGTTGCTCC 59.132 37.037 0.00 0.00 0.00 4.70
854 859 9.202273 GTATAATAGAGAAGATTGTTGCTCCAG 57.798 37.037 0.00 0.00 0.00 3.86
855 860 5.690464 ATAGAGAAGATTGTTGCTCCAGT 57.310 39.130 0.00 0.00 0.00 4.00
856 861 3.936564 AGAGAAGATTGTTGCTCCAGTC 58.063 45.455 0.00 0.00 0.00 3.51
857 862 3.582208 AGAGAAGATTGTTGCTCCAGTCT 59.418 43.478 0.00 0.00 33.35 3.24
859 864 5.424895 AGAGAAGATTGTTGCTCCAGTCTAT 59.575 40.000 2.58 0.00 31.89 1.98
860 865 6.059787 AGAAGATTGTTGCTCCAGTCTATT 57.940 37.500 2.58 0.00 31.89 1.73
861 866 6.479884 AGAAGATTGTTGCTCCAGTCTATTT 58.520 36.000 2.58 0.00 31.89 1.40
862 867 6.944862 AGAAGATTGTTGCTCCAGTCTATTTT 59.055 34.615 2.58 0.00 31.89 1.82
863 868 7.449704 AGAAGATTGTTGCTCCAGTCTATTTTT 59.550 33.333 2.58 0.00 31.89 1.94
864 869 7.150783 AGATTGTTGCTCCAGTCTATTTTTC 57.849 36.000 0.56 0.00 30.54 2.29
865 870 6.944862 AGATTGTTGCTCCAGTCTATTTTTCT 59.055 34.615 0.56 0.00 30.54 2.52
866 871 6.959639 TTGTTGCTCCAGTCTATTTTTCTT 57.040 33.333 0.00 0.00 0.00 2.52
867 872 8.635765 ATTGTTGCTCCAGTCTATTTTTCTTA 57.364 30.769 0.00 0.00 0.00 2.10
868 873 8.458573 TTGTTGCTCCAGTCTATTTTTCTTAA 57.541 30.769 0.00 0.00 0.00 1.85
869 874 8.635765 TGTTGCTCCAGTCTATTTTTCTTAAT 57.364 30.769 0.00 0.00 0.00 1.40
870 875 8.730680 TGTTGCTCCAGTCTATTTTTCTTAATC 58.269 33.333 0.00 0.00 0.00 1.75
871 876 8.951243 GTTGCTCCAGTCTATTTTTCTTAATCT 58.049 33.333 0.00 0.00 0.00 2.40
872 877 9.520515 TTGCTCCAGTCTATTTTTCTTAATCTT 57.479 29.630 0.00 0.00 0.00 2.40
909 914 7.462571 AATCTGTTACAGGGGTAAAATTGTC 57.537 36.000 12.79 0.00 40.95 3.18
931 936 0.396417 AGATCTCCTCACCCACCTCG 60.396 60.000 0.00 0.00 0.00 4.63
1222 1227 3.024356 TCCTCGGCTCCCTCCTCT 61.024 66.667 0.00 0.00 0.00 3.69
1359 1364 2.752030 CTCCTCCACCACCTCATCTTA 58.248 52.381 0.00 0.00 0.00 2.10
1693 1698 0.374758 CACGGTGCTCGATGAAATGG 59.625 55.000 7.01 0.00 42.43 3.16
1752 1757 0.383983 CGCTGATCGCTGCTTATTGC 60.384 55.000 0.00 0.00 43.25 3.56
1796 1801 0.671781 GCGCTGGAGCTGAAGAAGAA 60.672 55.000 0.00 0.00 39.32 2.52
1948 1953 5.637810 CCGAACACAGTGACATACAATACTT 59.362 40.000 7.81 0.00 0.00 2.24
1983 1988 4.167652 TGTCATGCATGGTGATAATGGA 57.832 40.909 25.97 0.00 0.00 3.41
2179 2184 5.753438 GCGTTGATTCTTGGATACTGTATGA 59.247 40.000 4.79 0.00 37.61 2.15
2214 2219 1.333524 CGAGCACTGCAACTGTTGAAG 60.334 52.381 23.85 23.85 42.36 3.02
2354 2359 1.001641 GCATGGCTCCTGACAAGGT 60.002 57.895 0.00 0.00 44.82 3.50
2379 2384 7.758528 GTCTTATTGCATGAATTCTTTGAAGCT 59.241 33.333 7.05 0.00 0.00 3.74
2397 2402 5.471456 TGAAGCTCTCTCAAAGGCTAAAAAG 59.529 40.000 0.00 0.00 33.01 2.27
2414 2419 1.944177 AAGCTCCACCTAGCAGAAGA 58.056 50.000 0.00 0.00 45.30 2.87
2419 2424 3.030291 CTCCACCTAGCAGAAGATCTGT 58.970 50.000 8.97 0.00 45.94 3.41
2420 2425 2.762887 TCCACCTAGCAGAAGATCTGTG 59.237 50.000 8.97 0.00 45.94 3.66
2527 2532 4.701663 ACGCAGTGACCTCAATGG 57.298 55.556 5.01 0.00 42.51 3.16
2528 2533 2.057830 ACGCAGTGACCTCAATGGA 58.942 52.632 5.01 0.00 42.51 3.41
2545 2550 7.083062 TCAATGGAGCCTCATTAGAATGTAT 57.917 36.000 0.00 0.00 35.78 2.29
2557 2562 9.941664 CTCATTAGAATGTATGATTGGTTTGTC 57.058 33.333 2.32 0.00 37.65 3.18
2631 2636 1.227645 GCACATGCCTATGAGCGGA 60.228 57.895 0.00 0.00 40.23 5.54
2695 2701 5.053145 CCTGTAGGTAGCTGAATTGCTTAG 58.947 45.833 4.27 0.00 43.74 2.18
2734 2757 3.585862 AGCAAATGGAGTACTACGTGTG 58.414 45.455 12.66 12.66 0.00 3.82
2753 2776 3.558006 TGTGTACACAAAGATGTCAACCG 59.442 43.478 26.07 0.00 37.82 4.44
2760 2783 5.299279 ACACAAAGATGTCAACCGAGAATTT 59.701 36.000 0.00 0.00 37.82 1.82
2763 2786 6.697019 ACAAAGATGTCAACCGAGAATTTTTG 59.303 34.615 0.00 0.00 33.41 2.44
2847 2871 7.799081 TCCATTGACAGAGTATCAGATGAAAT 58.201 34.615 0.00 0.00 37.82 2.17
2862 2886 8.690203 TCAGATGAAATTCCACTAGTGAAAAA 57.310 30.769 24.68 14.76 0.00 1.94
2864 2888 9.565213 CAGATGAAATTCCACTAGTGAAAAATC 57.435 33.333 24.68 12.95 0.00 2.17
2908 2932 3.392285 AGCACCAGCACCATATCAGATAA 59.608 43.478 0.00 0.00 45.49 1.75
2951 2975 6.489603 TCTTGAAACCATCTAAAAGGCCATA 58.510 36.000 5.01 0.00 0.00 2.74
2954 2978 5.068987 TGAAACCATCTAAAAGGCCATATGC 59.931 40.000 5.01 0.00 40.16 3.14
2959 2983 2.703536 TCTAAAAGGCCATATGCTCGGA 59.296 45.455 5.01 0.00 40.92 4.55
2961 2985 2.664402 AAAGGCCATATGCTCGGATT 57.336 45.000 5.01 0.00 40.92 3.01
2975 2999 6.949578 TGCTCGGATTTTCAAATTCAAATC 57.050 33.333 8.31 8.31 38.27 2.17
3042 3066 4.043310 ACTGACATCCCCATTTTCTTCAGA 59.957 41.667 0.00 0.00 34.58 3.27
3054 3078 9.709495 CCCATTTTCTTCAGATTTTGAACATAA 57.291 29.630 0.00 0.00 40.82 1.90
3106 3130 5.841957 ATATGCCTCTCCACACAATTTTC 57.158 39.130 0.00 0.00 0.00 2.29
3196 3220 6.183360 CGTGCATGAAGAAGACAGATACAATT 60.183 38.462 0.00 0.00 0.00 2.32
3222 3247 9.996554 TTCTCTATCAACTATTCAACTGTGAAA 57.003 29.630 0.00 0.00 46.66 2.69
3340 3376 7.956328 AAGGAAAATAAATGTTACTCCCTCC 57.044 36.000 0.00 0.00 0.00 4.30
3341 3377 6.120220 AGGAAAATAAATGTTACTCCCTCCG 58.880 40.000 0.00 0.00 0.00 4.63
3342 3378 5.884232 GGAAAATAAATGTTACTCCCTCCGT 59.116 40.000 0.00 0.00 0.00 4.69
3343 3379 6.376299 GGAAAATAAATGTTACTCCCTCCGTT 59.624 38.462 0.00 0.00 0.00 4.44
3344 3380 6.997239 AAATAAATGTTACTCCCTCCGTTC 57.003 37.500 0.00 0.00 0.00 3.95
3345 3381 3.345508 AAATGTTACTCCCTCCGTTCC 57.654 47.619 0.00 0.00 0.00 3.62
3346 3382 0.822164 ATGTTACTCCCTCCGTTCCG 59.178 55.000 0.00 0.00 0.00 4.30
3347 3383 0.251297 TGTTACTCCCTCCGTTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
3348 3384 1.109609 GTTACTCCCTCCGTTCCGAT 58.890 55.000 0.00 0.00 0.00 4.18
3349 3385 1.479730 GTTACTCCCTCCGTTCCGATT 59.520 52.381 0.00 0.00 0.00 3.34
3350 3386 1.856629 TACTCCCTCCGTTCCGATTT 58.143 50.000 0.00 0.00 0.00 2.17
3351 3387 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
3352 3388 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
3353 3389 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
3354 3390 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
3356 3392 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
3357 3393 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
3358 3394 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
3359 3395 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
3360 3396 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
3361 3397 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
3362 3398 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
3363 3399 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
3364 3400 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
3365 3401 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
3366 3402 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
3367 3403 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
3368 3404 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
3369 3405 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
3370 3406 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
3371 3407 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
3372 3408 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
3373 3409 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
3374 3410 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
3375 3411 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
3376 3412 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
3377 3413 7.011295 ACTCGTCGTGGTTTTAGTTCAAATTTA 59.989 33.333 0.00 0.00 0.00 1.40
3378 3414 7.692088 TCGTCGTGGTTTTAGTTCAAATTTAA 58.308 30.769 0.00 0.00 0.00 1.52
3379 3415 8.180267 TCGTCGTGGTTTTAGTTCAAATTTAAA 58.820 29.630 0.00 0.00 0.00 1.52
3380 3416 8.254470 CGTCGTGGTTTTAGTTCAAATTTAAAC 58.746 33.333 0.00 0.00 0.00 2.01
3381 3417 9.292846 GTCGTGGTTTTAGTTCAAATTTAAACT 57.707 29.630 11.45 11.45 39.07 2.66
3392 3428 9.292846 AGTTCAAATTTAAACTAAAACCACGAC 57.707 29.630 4.83 0.00 34.05 4.34
3393 3429 7.895582 TCAAATTTAAACTAAAACCACGACG 57.104 32.000 0.00 0.00 0.00 5.12
3394 3430 7.692088 TCAAATTTAAACTAAAACCACGACGA 58.308 30.769 0.00 0.00 0.00 4.20
3395 3431 7.851963 TCAAATTTAAACTAAAACCACGACGAG 59.148 33.333 0.00 0.00 0.00 4.18
3396 3432 6.849588 ATTTAAACTAAAACCACGACGAGT 57.150 33.333 0.00 0.00 0.00 4.18
3397 3433 7.945033 ATTTAAACTAAAACCACGACGAGTA 57.055 32.000 0.00 0.00 0.00 2.59
3398 3434 7.763172 TTTAAACTAAAACCACGACGAGTAA 57.237 32.000 0.00 0.00 0.00 2.24
3399 3435 7.763172 TTAAACTAAAACCACGACGAGTAAA 57.237 32.000 0.00 0.00 0.00 2.01
3400 3436 6.849588 AAACTAAAACCACGACGAGTAAAT 57.150 33.333 0.00 0.00 0.00 1.40
3401 3437 6.457851 AACTAAAACCACGACGAGTAAATC 57.542 37.500 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.843334 AAAAACAATGAAACAAGTACGAAAGTA 57.157 25.926 0.00 0.00 46.88 2.24
12 13 8.042119 CGAAAAACAATGAAACAAGTACGAAAG 58.958 33.333 0.00 0.00 0.00 2.62
13 14 7.008447 CCGAAAAACAATGAAACAAGTACGAAA 59.992 33.333 0.00 0.00 0.00 3.46
14 15 6.469595 CCGAAAAACAATGAAACAAGTACGAA 59.530 34.615 0.00 0.00 0.00 3.85
15 16 5.966503 CCGAAAAACAATGAAACAAGTACGA 59.033 36.000 0.00 0.00 0.00 3.43
16 17 5.740099 ACCGAAAAACAATGAAACAAGTACG 59.260 36.000 0.00 0.00 0.00 3.67
17 18 7.514573 AACCGAAAAACAATGAAACAAGTAC 57.485 32.000 0.00 0.00 0.00 2.73
18 19 7.063544 CCAAACCGAAAAACAATGAAACAAGTA 59.936 33.333 0.00 0.00 0.00 2.24
19 20 6.128418 CCAAACCGAAAAACAATGAAACAAGT 60.128 34.615 0.00 0.00 0.00 3.16
20 21 6.247176 CCAAACCGAAAAACAATGAAACAAG 58.753 36.000 0.00 0.00 0.00 3.16
21 22 5.390991 GCCAAACCGAAAAACAATGAAACAA 60.391 36.000 0.00 0.00 0.00 2.83
22 23 4.093556 GCCAAACCGAAAAACAATGAAACA 59.906 37.500 0.00 0.00 0.00 2.83
23 24 4.331443 AGCCAAACCGAAAAACAATGAAAC 59.669 37.500 0.00 0.00 0.00 2.78
24 25 4.508662 AGCCAAACCGAAAAACAATGAAA 58.491 34.783 0.00 0.00 0.00 2.69
25 26 4.130286 AGCCAAACCGAAAAACAATGAA 57.870 36.364 0.00 0.00 0.00 2.57
26 27 3.810310 AGCCAAACCGAAAAACAATGA 57.190 38.095 0.00 0.00 0.00 2.57
27 28 3.620821 ACAAGCCAAACCGAAAAACAATG 59.379 39.130 0.00 0.00 0.00 2.82
28 29 3.867857 ACAAGCCAAACCGAAAAACAAT 58.132 36.364 0.00 0.00 0.00 2.71
29 30 3.320673 ACAAGCCAAACCGAAAAACAA 57.679 38.095 0.00 0.00 0.00 2.83
30 31 4.451629 TTACAAGCCAAACCGAAAAACA 57.548 36.364 0.00 0.00 0.00 2.83
31 32 5.349270 ACTTTTACAAGCCAAACCGAAAAAC 59.651 36.000 0.00 0.00 32.57 2.43
32 33 5.480205 ACTTTTACAAGCCAAACCGAAAAA 58.520 33.333 0.00 0.00 32.57 1.94
33 34 5.074584 ACTTTTACAAGCCAAACCGAAAA 57.925 34.783 0.00 0.00 32.57 2.29
34 35 4.722361 ACTTTTACAAGCCAAACCGAAA 57.278 36.364 0.00 0.00 32.57 3.46
35 36 5.299782 ACATACTTTTACAAGCCAAACCGAA 59.700 36.000 0.00 0.00 32.57 4.30
36 37 4.822896 ACATACTTTTACAAGCCAAACCGA 59.177 37.500 0.00 0.00 32.57 4.69
37 38 5.116069 ACATACTTTTACAAGCCAAACCG 57.884 39.130 0.00 0.00 32.57 4.44
38 39 5.924254 GGAACATACTTTTACAAGCCAAACC 59.076 40.000 0.00 0.00 32.57 3.27
39 40 5.627780 CGGAACATACTTTTACAAGCCAAAC 59.372 40.000 0.00 0.00 32.57 2.93
40 41 5.299782 ACGGAACATACTTTTACAAGCCAAA 59.700 36.000 0.00 0.00 32.57 3.28
41 42 4.822896 ACGGAACATACTTTTACAAGCCAA 59.177 37.500 0.00 0.00 32.57 4.52
42 43 4.391155 ACGGAACATACTTTTACAAGCCA 58.609 39.130 0.00 0.00 32.57 4.75
43 44 5.151389 CAACGGAACATACTTTTACAAGCC 58.849 41.667 0.00 0.00 32.57 4.35
44 45 5.754778 ACAACGGAACATACTTTTACAAGC 58.245 37.500 0.00 0.00 32.57 4.01
45 46 9.887406 AATAACAACGGAACATACTTTTACAAG 57.113 29.630 0.00 0.00 35.92 3.16
50 51 9.974980 ATGAAAATAACAACGGAACATACTTTT 57.025 25.926 0.00 0.00 0.00 2.27
51 52 9.974980 AATGAAAATAACAACGGAACATACTTT 57.025 25.926 0.00 0.00 0.00 2.66
52 53 9.620660 GAATGAAAATAACAACGGAACATACTT 57.379 29.630 0.00 0.00 0.00 2.24
53 54 9.010029 AGAATGAAAATAACAACGGAACATACT 57.990 29.630 0.00 0.00 0.00 2.12
54 55 9.620660 AAGAATGAAAATAACAACGGAACATAC 57.379 29.630 0.00 0.00 0.00 2.39
56 57 9.840427 CTAAGAATGAAAATAACAACGGAACAT 57.160 29.630 0.00 0.00 0.00 2.71
57 58 8.293867 CCTAAGAATGAAAATAACAACGGAACA 58.706 33.333 0.00 0.00 0.00 3.18
58 59 7.272731 GCCTAAGAATGAAAATAACAACGGAAC 59.727 37.037 0.00 0.00 0.00 3.62
59 60 7.175990 AGCCTAAGAATGAAAATAACAACGGAA 59.824 33.333 0.00 0.00 0.00 4.30
60 61 6.657541 AGCCTAAGAATGAAAATAACAACGGA 59.342 34.615 0.00 0.00 0.00 4.69
61 62 6.852664 AGCCTAAGAATGAAAATAACAACGG 58.147 36.000 0.00 0.00 0.00 4.44
62 63 8.742554 AAAGCCTAAGAATGAAAATAACAACG 57.257 30.769 0.00 0.00 0.00 4.10
84 85 9.399403 GAAAAGTCTGGCTTTGAACTAATAAAG 57.601 33.333 8.18 0.00 45.91 1.85
85 86 9.131791 AGAAAAGTCTGGCTTTGAACTAATAAA 57.868 29.630 8.18 0.00 45.91 1.40
86 87 8.691661 AGAAAAGTCTGGCTTTGAACTAATAA 57.308 30.769 8.18 0.00 45.91 1.40
87 88 8.691661 AAGAAAAGTCTGGCTTTGAACTAATA 57.308 30.769 8.18 0.00 45.91 0.98
88 89 7.588497 AAGAAAAGTCTGGCTTTGAACTAAT 57.412 32.000 8.18 0.00 45.91 1.73
89 90 7.257722 CAAAGAAAAGTCTGGCTTTGAACTAA 58.742 34.615 8.18 0.00 45.91 2.24
90 91 6.183360 CCAAAGAAAAGTCTGGCTTTGAACTA 60.183 38.462 8.18 0.00 45.91 2.24
91 92 5.394553 CCAAAGAAAAGTCTGGCTTTGAACT 60.395 40.000 8.18 5.88 45.91 3.01
92 93 4.805719 CCAAAGAAAAGTCTGGCTTTGAAC 59.194 41.667 8.18 3.73 45.91 3.18
93 94 4.680440 GCCAAAGAAAAGTCTGGCTTTGAA 60.680 41.667 8.18 0.00 45.91 2.69
94 95 3.181476 GCCAAAGAAAAGTCTGGCTTTGA 60.181 43.478 8.18 0.00 45.91 2.69
95 96 3.126073 GCCAAAGAAAAGTCTGGCTTTG 58.874 45.455 8.18 0.00 45.91 2.77
97 98 1.688735 GGCCAAAGAAAAGTCTGGCTT 59.311 47.619 11.42 0.00 40.97 4.35
98 99 1.133356 AGGCCAAAGAAAAGTCTGGCT 60.133 47.619 5.01 0.00 40.97 4.75
99 100 1.332195 AGGCCAAAGAAAAGTCTGGC 58.668 50.000 5.01 3.29 40.63 4.85
100 101 3.638627 AGAAAGGCCAAAGAAAAGTCTGG 59.361 43.478 5.01 0.00 33.05 3.86
101 102 4.261783 GGAGAAAGGCCAAAGAAAAGTCTG 60.262 45.833 5.01 0.00 33.05 3.51
102 103 3.891977 GGAGAAAGGCCAAAGAAAAGTCT 59.108 43.478 5.01 0.00 34.72 3.24
103 104 3.636764 TGGAGAAAGGCCAAAGAAAAGTC 59.363 43.478 5.01 0.00 31.13 3.01
104 105 3.384789 GTGGAGAAAGGCCAAAGAAAAGT 59.615 43.478 5.01 0.00 37.12 2.66
105 106 3.550842 CGTGGAGAAAGGCCAAAGAAAAG 60.551 47.826 5.01 0.00 37.12 2.27
106 107 2.360801 CGTGGAGAAAGGCCAAAGAAAA 59.639 45.455 5.01 0.00 37.12 2.29
107 108 1.953686 CGTGGAGAAAGGCCAAAGAAA 59.046 47.619 5.01 0.00 37.12 2.52
108 109 1.604604 CGTGGAGAAAGGCCAAAGAA 58.395 50.000 5.01 0.00 37.12 2.52
109 110 0.250727 CCGTGGAGAAAGGCCAAAGA 60.251 55.000 5.01 0.00 37.12 2.52
110 111 1.244019 CCCGTGGAGAAAGGCCAAAG 61.244 60.000 5.01 0.00 37.12 2.77
111 112 1.228429 CCCGTGGAGAAAGGCCAAA 60.228 57.895 5.01 0.00 37.12 3.28
112 113 2.434331 CCCGTGGAGAAAGGCCAA 59.566 61.111 5.01 0.00 37.12 4.52
113 114 3.646715 CCCCGTGGAGAAAGGCCA 61.647 66.667 5.01 0.00 0.00 5.36
115 116 3.978571 GAGCCCCGTGGAGAAAGGC 62.979 68.421 0.00 0.00 44.20 4.35
116 117 2.269241 GAGCCCCGTGGAGAAAGG 59.731 66.667 0.00 0.00 0.00 3.11
117 118 1.376037 GTGAGCCCCGTGGAGAAAG 60.376 63.158 0.00 0.00 0.00 2.62
118 119 2.747686 GTGAGCCCCGTGGAGAAA 59.252 61.111 0.00 0.00 0.00 2.52
119 120 3.691342 CGTGAGCCCCGTGGAGAA 61.691 66.667 0.00 0.00 0.00 2.87
120 121 4.988716 ACGTGAGCCCCGTGGAGA 62.989 66.667 0.00 0.00 37.12 3.71
121 122 3.530910 AAACGTGAGCCCCGTGGAG 62.531 63.158 0.00 0.00 38.77 3.86
122 123 3.524648 GAAACGTGAGCCCCGTGGA 62.525 63.158 0.00 0.00 38.77 4.02
123 124 2.162338 TAGAAACGTGAGCCCCGTGG 62.162 60.000 0.00 0.00 38.77 4.94
124 125 0.108329 ATAGAAACGTGAGCCCCGTG 60.108 55.000 0.00 0.00 38.77 4.94
125 126 1.407979 CTATAGAAACGTGAGCCCCGT 59.592 52.381 0.00 0.00 40.92 5.28
126 127 1.407979 ACTATAGAAACGTGAGCCCCG 59.592 52.381 6.78 0.00 0.00 5.73
127 128 3.635836 AGTACTATAGAAACGTGAGCCCC 59.364 47.826 6.78 0.00 0.00 5.80
128 129 4.608951 CAGTACTATAGAAACGTGAGCCC 58.391 47.826 6.78 0.00 0.00 5.19
129 130 4.043073 GCAGTACTATAGAAACGTGAGCC 58.957 47.826 6.78 0.00 0.00 4.70
130 131 4.669318 TGCAGTACTATAGAAACGTGAGC 58.331 43.478 6.78 8.98 0.00 4.26
131 132 9.464714 AATATTGCAGTACTATAGAAACGTGAG 57.535 33.333 6.78 0.12 0.00 3.51
146 147 9.929722 CGCTTCTAACAAATTAATATTGCAGTA 57.070 29.630 0.00 0.00 0.00 2.74
147 148 7.432252 GCGCTTCTAACAAATTAATATTGCAGT 59.568 33.333 0.00 0.00 0.00 4.40
148 149 7.431960 TGCGCTTCTAACAAATTAATATTGCAG 59.568 33.333 9.73 7.61 0.00 4.41
149 150 7.254137 TGCGCTTCTAACAAATTAATATTGCA 58.746 30.769 9.73 0.00 0.00 4.08
150 151 7.678194 TGCGCTTCTAACAAATTAATATTGC 57.322 32.000 9.73 0.00 0.00 3.56
154 155 9.449550 CATGATTGCGCTTCTAACAAATTAATA 57.550 29.630 9.73 0.00 0.00 0.98
155 156 7.043192 GCATGATTGCGCTTCTAACAAATTAAT 60.043 33.333 9.73 0.00 39.49 1.40
156 157 6.253298 GCATGATTGCGCTTCTAACAAATTAA 59.747 34.615 9.73 0.00 39.49 1.40
157 158 5.743398 GCATGATTGCGCTTCTAACAAATTA 59.257 36.000 9.73 0.00 39.49 1.40
158 159 4.563976 GCATGATTGCGCTTCTAACAAATT 59.436 37.500 9.73 0.00 39.49 1.82
159 160 4.107622 GCATGATTGCGCTTCTAACAAAT 58.892 39.130 9.73 0.00 39.49 2.32
160 161 3.500982 GCATGATTGCGCTTCTAACAAA 58.499 40.909 9.73 0.00 39.49 2.83
161 162 3.135414 GCATGATTGCGCTTCTAACAA 57.865 42.857 9.73 0.00 39.49 2.83
162 163 2.830772 GCATGATTGCGCTTCTAACA 57.169 45.000 9.73 0.74 39.49 2.41
172 173 4.841443 TCATGATAAGTGGCATGATTGC 57.159 40.909 0.00 0.00 44.17 3.56
176 177 6.829811 TCATCTTTTCATGATAAGTGGCATGA 59.170 34.615 20.83 18.61 46.50 3.07
177 178 6.916387 GTCATCTTTTCATGATAAGTGGCATG 59.084 38.462 20.83 17.13 42.41 4.06
178 179 6.832384 AGTCATCTTTTCATGATAAGTGGCAT 59.168 34.615 20.83 8.34 35.23 4.40
179 180 6.182627 AGTCATCTTTTCATGATAAGTGGCA 58.817 36.000 20.83 6.63 35.23 4.92
180 181 6.690194 AGTCATCTTTTCATGATAAGTGGC 57.310 37.500 20.83 18.71 35.23 5.01
181 182 8.503458 AGAAGTCATCTTTTCATGATAAGTGG 57.497 34.615 20.83 15.35 35.23 4.00
182 183 9.770503 CAAGAAGTCATCTTTTCATGATAAGTG 57.229 33.333 20.83 17.85 46.39 3.16
183 184 9.730705 TCAAGAAGTCATCTTTTCATGATAAGT 57.269 29.630 20.83 9.44 46.39 2.24
194 195 9.829507 CTGTTCCTATATCAAGAAGTCATCTTT 57.170 33.333 0.00 0.00 46.39 2.52
196 197 8.546083 ACTGTTCCTATATCAAGAAGTCATCT 57.454 34.615 0.00 0.00 41.32 2.90
197 198 7.593273 CGACTGTTCCTATATCAAGAAGTCATC 59.407 40.741 0.00 0.00 0.00 2.92
198 199 7.068839 ACGACTGTTCCTATATCAAGAAGTCAT 59.931 37.037 0.00 0.00 0.00 3.06
199 200 6.377429 ACGACTGTTCCTATATCAAGAAGTCA 59.623 38.462 0.00 0.00 0.00 3.41
200 201 6.797454 ACGACTGTTCCTATATCAAGAAGTC 58.203 40.000 0.00 0.00 0.00 3.01
201 202 6.458478 CGACGACTGTTCCTATATCAAGAAGT 60.458 42.308 0.00 0.00 0.00 3.01
202 203 5.910166 CGACGACTGTTCCTATATCAAGAAG 59.090 44.000 0.00 0.00 0.00 2.85
224 225 2.610976 CCAAAAGTACCCATGACGACGA 60.611 50.000 0.00 0.00 0.00 4.20
229 230 3.009143 AGGAGACCAAAAGTACCCATGAC 59.991 47.826 0.00 0.00 0.00 3.06
234 235 2.160205 GCAAGGAGACCAAAAGTACCC 58.840 52.381 0.00 0.00 0.00 3.69
236 237 3.075148 GAGGCAAGGAGACCAAAAGTAC 58.925 50.000 0.00 0.00 0.00 2.73
252 253 2.862432 CCAAGATGGTAGCAGGAGGCA 61.862 57.143 0.00 0.00 37.65 4.75
263 264 3.376935 CTCTCGGCGCCAAGATGGT 62.377 63.158 28.98 0.00 40.46 3.55
275 276 4.787280 AGGCCCTCCACCTCTCGG 62.787 72.222 0.00 0.00 28.76 4.63
289 291 3.756963 ACAAAACCTTAAAGATCGGAGGC 59.243 43.478 6.62 0.00 32.42 4.70
294 296 4.497473 TGCCACAAAACCTTAAAGATCG 57.503 40.909 0.00 0.00 0.00 3.69
310 312 8.671921 CAAATATAGATCACCAATAGATGCCAC 58.328 37.037 0.00 0.00 0.00 5.01
351 354 3.428534 GGCACCGCAAAATAAAACAAGAG 59.571 43.478 0.00 0.00 0.00 2.85
356 359 2.474816 TGTGGCACCGCAAAATAAAAC 58.525 42.857 16.26 0.00 33.12 2.43
437 441 7.497925 AACCAACAAAAACAACTTAAAGCAA 57.502 28.000 0.00 0.00 0.00 3.91
526 530 5.777223 CCAGTGATGATATCCTAGAAGTCCA 59.223 44.000 0.00 0.00 0.00 4.02
528 532 5.480073 AGCCAGTGATGATATCCTAGAAGTC 59.520 44.000 0.00 0.00 0.00 3.01
530 534 5.479724 TGAGCCAGTGATGATATCCTAGAAG 59.520 44.000 0.00 0.00 0.00 2.85
574 578 5.904362 ACCTATCCAAAAAGATGCAAGAC 57.096 39.130 0.00 0.00 0.00 3.01
575 579 7.175104 AGTTACCTATCCAAAAAGATGCAAGA 58.825 34.615 0.00 0.00 0.00 3.02
586 591 3.120108 CCCCCTGAGTTACCTATCCAAA 58.880 50.000 0.00 0.00 0.00 3.28
593 598 2.424793 TGAAAACCCCCTGAGTTACCT 58.575 47.619 0.00 0.00 0.00 3.08
749 754 5.745312 AGAATCACAGTGGTATCTGTTGA 57.255 39.130 0.00 0.00 44.92 3.18
753 758 6.873605 TGTGTTAAGAATCACAGTGGTATCTG 59.126 38.462 0.00 0.00 39.23 2.90
766 771 6.798959 GCAAAGTGAGTCATGTGTTAAGAATC 59.201 38.462 0.00 0.00 0.00 2.52
776 781 8.362639 AGAAAAATAATGCAAAGTGAGTCATGT 58.637 29.630 0.00 0.00 0.00 3.21
777 782 8.752766 AGAAAAATAATGCAAAGTGAGTCATG 57.247 30.769 0.00 0.00 0.00 3.07
800 805 8.635765 ACACTGCTTTGGATTTTAAGATTAGA 57.364 30.769 0.00 0.00 0.00 2.10
801 806 9.774742 GTACACTGCTTTGGATTTTAAGATTAG 57.225 33.333 0.00 0.00 0.00 1.73
803 808 7.040686 ACGTACACTGCTTTGGATTTTAAGATT 60.041 33.333 0.00 0.00 0.00 2.40
827 832 7.867909 TGGAGCAACAATCTTCTCTATTATACG 59.132 37.037 0.00 0.00 0.00 3.06
837 842 5.690464 ATAGACTGGAGCAACAATCTTCT 57.310 39.130 0.00 0.00 0.00 2.85
838 843 6.749923 AAATAGACTGGAGCAACAATCTTC 57.250 37.500 0.00 0.00 0.00 2.87
840 845 6.944862 AGAAAAATAGACTGGAGCAACAATCT 59.055 34.615 0.00 0.00 0.00 2.40
843 848 6.959639 AAGAAAAATAGACTGGAGCAACAA 57.040 33.333 0.00 0.00 0.00 2.83
845 850 8.951243 AGATTAAGAAAAATAGACTGGAGCAAC 58.049 33.333 0.00 0.00 0.00 4.17
882 887 8.710239 ACAATTTTACCCCTGTAACAGATTTTT 58.290 29.630 0.00 0.00 36.69 1.94
883 888 8.257602 ACAATTTTACCCCTGTAACAGATTTT 57.742 30.769 0.00 0.00 36.69 1.82
909 914 1.912043 AGGTGGGTGAGGAGATCTTTG 59.088 52.381 0.00 0.00 0.00 2.77
931 936 4.498520 TCGCTAGCAGTCGCAGGC 62.499 66.667 16.45 0.00 42.27 4.85
943 948 4.111016 CCGTGGCAGTCGTCGCTA 62.111 66.667 0.00 0.00 0.00 4.26
1128 1133 2.295602 TTGGGGTAGGAAGCGGGAC 61.296 63.158 0.00 0.00 0.00 4.46
1245 1250 2.066999 GTGGAGGAGGAGGGCGAAT 61.067 63.158 0.00 0.00 0.00 3.34
1407 1412 2.126965 AAGAGAACGTCGACGGCG 60.127 61.111 37.89 21.79 44.95 6.46
1752 1757 1.077930 CAGACCACCATGCTCCCTG 60.078 63.158 0.00 0.00 0.00 4.45
1754 1759 1.852157 TTCCAGACCACCATGCTCCC 61.852 60.000 0.00 0.00 0.00 4.30
1796 1801 1.966148 TAGCCCCTCCAGCTCCATCT 61.966 60.000 0.00 0.00 41.83 2.90
1948 1953 6.015265 CCATGCATGACATACCCATAAATCAA 60.015 38.462 28.31 0.00 36.64 2.57
1983 1988 3.254024 ATGAACCCTCCGCGCTGTT 62.254 57.895 5.56 0.00 0.00 3.16
1990 1995 0.839946 ATCCCTTCATGAACCCTCCG 59.160 55.000 3.38 0.00 0.00 4.63
2272 2277 7.092716 TCAAAATCCTTATTCTTGCAGAAAGC 58.907 34.615 3.27 0.00 37.82 3.51
2354 2359 7.833786 AGCTTCAAAGAATTCATGCAATAAGA 58.166 30.769 8.44 0.00 0.00 2.10
2379 2384 4.202461 TGGAGCTTTTTAGCCTTTGAGAGA 60.202 41.667 0.00 0.00 34.90 3.10
2397 2402 2.038659 AGATCTTCTGCTAGGTGGAGC 58.961 52.381 0.00 0.00 43.16 4.70
2414 2419 3.521126 ACCTTTATCAGCTGACCACAGAT 59.479 43.478 20.97 3.44 46.03 2.90
2419 2424 2.265367 TCCACCTTTATCAGCTGACCA 58.735 47.619 20.97 7.21 0.00 4.02
2420 2425 3.350219 TTCCACCTTTATCAGCTGACC 57.650 47.619 20.97 0.00 0.00 4.02
2516 2521 1.588239 ATGAGGCTCCATTGAGGTCA 58.412 50.000 12.86 0.00 39.14 4.02
2527 2532 6.939163 ACCAATCATACATTCTAATGAGGCTC 59.061 38.462 7.79 7.79 39.67 4.70
2528 2533 6.845908 ACCAATCATACATTCTAATGAGGCT 58.154 36.000 9.60 0.00 39.67 4.58
2545 2550 4.163441 TGTTCTCCAGACAAACCAATCA 57.837 40.909 0.00 0.00 0.00 2.57
2557 2562 9.454859 AAGGATTTAAGTTCTATTGTTCTCCAG 57.545 33.333 0.00 0.00 0.00 3.86
2613 2618 0.604780 ATCCGCTCATAGGCATGTGC 60.605 55.000 11.40 11.40 44.50 4.57
2631 2636 7.287696 AGGTTGTCTTCATTTAACCAAACAGAT 59.712 33.333 0.00 0.00 43.84 2.90
2695 2701 3.020274 TGCTACAGTCATCTCTCAGGAC 58.980 50.000 0.00 0.00 0.00 3.85
2734 2757 4.304110 TCTCGGTTGACATCTTTGTGTAC 58.696 43.478 0.00 0.00 35.79 2.90
2760 2783 8.985315 AACTCCATAAGCATCTGATTATCAAA 57.015 30.769 0.00 0.00 34.75 2.69
2763 2786 9.149225 CTGTAACTCCATAAGCATCTGATTATC 57.851 37.037 0.00 0.00 34.75 1.75
2847 2871 7.737972 TCAATTCGATTTTTCACTAGTGGAA 57.262 32.000 22.48 17.88 0.00 3.53
2862 2886 2.091541 ACCGGCACAAATCAATTCGAT 58.908 42.857 0.00 0.00 35.12 3.59
2864 2888 2.095263 AGAACCGGCACAAATCAATTCG 60.095 45.455 0.00 0.00 0.00 3.34
2879 2903 1.741770 GGTGCTGGTGCTAGAACCG 60.742 63.158 15.59 10.92 43.73 4.44
2908 2932 5.766670 TCAAGAAGATGTTTGAAGTGAGCAT 59.233 36.000 0.00 0.00 30.84 3.79
2951 2975 7.529880 GATTTGAATTTGAAAATCCGAGCAT 57.470 32.000 9.42 0.00 36.99 3.79
2975 2999 7.599998 CAGAAATTTTCCTCCAATACAAACTGG 59.400 37.037 5.52 0.00 0.00 4.00
3025 3049 7.016465 TGTTCAAAATCTGAAGAAAATGGGGAT 59.984 33.333 0.00 0.00 44.83 3.85
3054 3078 4.142513 GGAGAACCACGACGTCTTATAAGT 60.143 45.833 14.70 0.00 35.97 2.24
3067 3091 4.511826 GGCATATAAAAGAGGAGAACCACG 59.488 45.833 0.00 0.00 38.94 4.94
3164 3188 3.002791 TCTTCTTCATGCACGATGGTTC 58.997 45.455 0.00 0.00 32.26 3.62
3171 3195 4.176271 TGTATCTGTCTTCTTCATGCACG 58.824 43.478 0.00 0.00 0.00 5.34
3196 3220 9.996554 TTTCACAGTTGAATAGTTGATAGAGAA 57.003 29.630 0.00 0.00 41.50 2.87
3325 3361 3.345508 GGAACGGAGGGAGTAACATTT 57.654 47.619 0.00 0.00 0.00 2.32
3346 3382 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
3347 3383 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
3348 3384 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
3349 3385 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
3350 3386 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
3351 3387 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
3352 3388 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
3353 3389 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
3354 3390 7.895582 TTAAATTTGAACTAAAACCACGACG 57.104 32.000 0.00 0.00 0.00 5.12
3355 3391 9.292846 AGTTTAAATTTGAACTAAAACCACGAC 57.707 29.630 22.70 0.00 35.55 4.34
3366 3402 9.292846 GTCGTGGTTTTAGTTTAAATTTGAACT 57.707 29.630 25.84 25.84 39.80 3.01
3367 3403 8.254470 CGTCGTGGTTTTAGTTTAAATTTGAAC 58.746 33.333 15.93 15.93 0.00 3.18
3368 3404 8.180267 TCGTCGTGGTTTTAGTTTAAATTTGAA 58.820 29.630 0.00 0.00 0.00 2.69
3369 3405 7.692088 TCGTCGTGGTTTTAGTTTAAATTTGA 58.308 30.769 0.00 0.00 0.00 2.69
3370 3406 7.641020 ACTCGTCGTGGTTTTAGTTTAAATTTG 59.359 33.333 0.00 0.00 0.00 2.32
3371 3407 7.696755 ACTCGTCGTGGTTTTAGTTTAAATTT 58.303 30.769 0.00 0.00 0.00 1.82
3372 3408 7.250445 ACTCGTCGTGGTTTTAGTTTAAATT 57.750 32.000 0.00 0.00 0.00 1.82
3373 3409 6.849588 ACTCGTCGTGGTTTTAGTTTAAAT 57.150 33.333 0.00 0.00 0.00 1.40
3374 3410 7.763172 TTACTCGTCGTGGTTTTAGTTTAAA 57.237 32.000 0.00 0.00 0.00 1.52
3375 3411 7.763172 TTTACTCGTCGTGGTTTTAGTTTAA 57.237 32.000 0.00 0.00 0.00 1.52
3376 3412 7.148983 CGATTTACTCGTCGTGGTTTTAGTTTA 60.149 37.037 0.00 0.00 42.56 2.01
3377 3413 6.346040 CGATTTACTCGTCGTGGTTTTAGTTT 60.346 38.462 0.00 0.00 42.56 2.66
3378 3414 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
3379 3415 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
3380 3416 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
3381 3417 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
3382 3418 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
3383 3419 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
3384 3420 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
3385 3421 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
3386 3422 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
3387 3423 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
3388 3424 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
3389 3425 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
3390 3426 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
3391 3427 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
3393 3429 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
3394 3430 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
3395 3431 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
3396 3432 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
3397 3433 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
3398 3434 1.341778 ACTACTCCCTCCGTTCCGATT 60.342 52.381 0.00 0.00 0.00 3.34
3399 3435 0.258194 ACTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18
3400 3436 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3401 3437 1.307097 CTACTACTCCCTCCGTTCCG 58.693 60.000 0.00 0.00 0.00 4.30
3402 3438 1.031235 GCTACTACTCCCTCCGTTCC 58.969 60.000 0.00 0.00 0.00 3.62
3403 3439 2.055684 AGCTACTACTCCCTCCGTTC 57.944 55.000 0.00 0.00 0.00 3.95
3404 3440 2.528673 AAGCTACTACTCCCTCCGTT 57.471 50.000 0.00 0.00 0.00 4.44
3405 3441 2.291411 TGAAAGCTACTACTCCCTCCGT 60.291 50.000 0.00 0.00 0.00 4.69
3406 3442 2.359531 CTGAAAGCTACTACTCCCTCCG 59.640 54.545 0.00 0.00 0.00 4.63


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.